If you want mechjeb to do a rendezvous with another rocket, you need to launch a rocket and then,launch the same rocket and it will rendezvous with the first rocket.
It would be great if we wouldn't need that.
How?
Simple( I am talking about the concept,not the programation):when you launch a rocket(for better comprehension we will name it x), mechjeb would save the data as if it were a practice launch in a specific file for that rocket.
In that way,if you launch a different rocket and then launch the rocket x,mechjeb would have the data for the rendezvous saved for that rocket.
You would still have to do a practice launch for all the rockets,but at least you could rendezvous two different rocket,wich would be very nice for 0.18!